ABI CellML Meeting Minutes, 24th November 2010
Present: Dougal Cowan, Mona Zhu, Amy You, Michael Backhaus, Andrew Miller, Randall Britten, David "Andre" Nickerson, Lukas Endler
This week's agenda:
0) Introductions - Lukas, Mona, Amy
Discussion:
- Lukas and the new summer students Mona and Amy introduced themselves.
1) Repository contributions - update
Progress:
- Dougal: have exposed 3 recently pushed models - Gerard et al. 2005, Garmendia-Torres et al. 2007, and Houart et al. 1999. Dougal will be creating exposures in the interim until a new system is in place.
- Amy: has coded up the Swat 2004 model in CellML and pushed it to the repository.
- Camille: has coded up and pushed Goldbeter et al. 2007 and Gérard C, Goldbeter A, 2009.
- Mona: has coded up and pushed Houart et al. 1999, Garmendia-Torres et al. 2007, and Conradie et al. 2010.
2) PMR2 development - update
- Tommy is on leave. No update.
3) CellML API - update
Progress:
- Andrew: still working on TeLICeMS - the parser is essentiall complete. A test suite with a trivial example has been created, which converts from CellML to TeLICeMS. The other direction will need some more work, and then round-trip testing can be performed.
Discussion:
- There was a discussion about API features: order preservation, comments, and the TeLICeMS service.
Action item 1: Randall to get in touch with Alan to discuss the TeLICeMS service and text input in OpenCell.
4) CellML API survey
Progress:
- Dougal: has created a Google Forms survey which is basically complete, but still has a few problems. Needs assistance with the ethics approval process.
Discussion:
- There was a discussion about the survey form. A breakaway was called to further discuss this.
5) CellML core specs - update
Progress:
- Andrew: ModML - still working on the Rice 2008 model. To get it working, symbolic differentiation has to be performed.
Discussion:
- There was a discussion about how ModML works.
6) Encyclopedia article (CellML language)
Progress:
- Andrew: Poul is happy with the latest version sent by Andrew.
- Randall: still have a few minor changes to send.
7) Time permitting: Updates or additional items from volunteering attendees
- Randall: the article on using OpenCell to generate MATLAB code has been published:
http://www.benthamscience.com/open/topetj/articles/V003/SI0001TOPETJ/60TOPETJ.htm